Identification of growth-related SNPs and genes in the genome of the Pacific abalone (Haliotis discus hannai) using GWAS

The Pacific abalone, Haliotis discus hannai, is the economically important aquaculture species along coast regions of southeast China. However, the slow growth of abalone species impedes the health development of the abalone farming industry. In this study, the genome-wide association study (GWAS) for the growth related traits in Pacific abalone was performed. Genetic parameters of 10 growth-related traits in 222 individuals of the Pacific abalone were estimated by using 1,431,014 single nucleotide polymorphisms (SNPs) detected by whole genome resequencing (WGS). A total of 263 significant SNPs associated with growth traits were identified. Seven of these SNPs were further shown to be reliable growth-associated markers in a new validation population containing 1059 samples. In addition, 62 genes, including fgfr2, bmp7, cubn, rala, gpam, and adamts9, harboring significant markers were considered candidate genes, which may affect growth-related traits associated with various biological processes, such as cell proliferation, glycometabolism, and lipid metabolism. Our results will not only improve our understanding of the genetic architecture of abalone growth traits but also provide valuable SNPs for the marker-assisted selection and breeding of the Pacific abalone. •The first genome-wide association study (GWAS) for growth-related traits was performed in abalone.•Heritability of the 10 traits was estimated using the GBLUP, which is more accurate than previous studies in abalone.•Whole genome resequencing (WGS) was used to capture SNP markers close to the actual causal mutations in Pacific abalone.•Significant SNPs identified by GWAS were further verified in a larger population with 1059 samples.